sknano.core.atoms.XAtoms

class sknano.core.atoms.XAtoms(atoms=None, copylist=True, deepcopy=False)

An eXtended Atoms class.

Sub-class of Atoms class, and a container class for lists of XAtom instances.

Parameters:

atoms : {None, sequence, XAtoms}, optional

if not None, then a list of XAtom instance objects or an existing XAtoms instance object.

copylist : bool, optional

perform shallow copy of atoms list

deepcopy : bool, optional

perform deepcopy of atoms list

Attributes

CM	Center-of-Mass coordinates of Atoms.
M	Total mass of Atoms.
Natoms	Number of atoms in Atoms.
Ntypes	Number of atomtypes.
atom_ids	Return array of XAtom IDs.
atomtypes	atomtypes dict.
bounds	Bounds of Atoms.
centroid	Centroid of Atoms.
charges	Return array of XAtom charges.
coords	numpy.ndarray of Atoms \(x, y, z\) coordinates.
inertia_tensor	Return the inertia tensor.
masses	Return list of Atom masses.
q	Return the total net charge of XAtoms.
symbols	Return list of Atom symbols.
velocities	Return array of XAtom velocities.
x	numpy.ndarray of Atoms \(x\) coordinates.
y	numpy.ndarray of Atoms \(y\) coordinates.
z	numpy.ndarray of Atoms \(z\) coordinates.

Methods

add_atomtype(atom)	Add atom type to atomtypes.
add_atomtypes([atoms])	Add atomtype for each atom in atoms to atomtypes dictionary.
append(item)
assign_unique_ids([starting_id])	Assign unique ID to each XAtom in XAtoms.
center_CM([axes])	Center atoms on CM coordinates.
clear()
clip_bounds(region[, center_before_clipping])	Remove atoms outside the given limits along given dimension.
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filter_ids(atom_ids[, invert])	Return Atoms by XAtoms.atom_ids in atom_ids.
get_atom(atomID)	Get XAtom with Xatom.atomID == atomID.
get_atoms([asarray])	Return list of Atoms.
get_coords([asdict])	Return atom coords.
getatomattr(attr)	Get numpy.ndarray of atom attributes attr.
index(item, *args)
insert(i, item)
mapatomattr(attr, from_attr, attrmap)	Set/update atom attribute from another atom attribute with dict.
pop([i])
remove(item)
reverse()
rezero([epsilon])	Set really really small coordinates to zero.
rezero_coords([epsilon])	Alias for Atoms.rezero.
rezero_xyz([epsilon])	Alias for Atoms.rezero.
rotate([angle, rot_axis, anchor_point, ...])	Rotate Atom position vectors.
select(cmd)
select_within(volume)
sort([key, reverse])
translate(t[, fix_anchor_points])	Translate Atom position vectors by Vector t.